Local-scale invasion pathways and small founder numbers in introduced Sacramento pikeminnow (Ptychocheilus grandis)
Conservation Genetics
Andrew P. Kinziger(1), Rodney J. Nakamoto(2), and Bret C. Harvey(2)
(1) Department of Fisheries Biology, Humboldt State University, One Harpst Street, Arcata, CA 95521
(2) U.S.D.A. Forest Service, Pacific Southwest Research Station-Arcata, 1700 Bayview Drive, Arcata, CA 95521
Corresponding author: Andrew P. Kinziger, Andrew.Kinziger@Humboldt.edu, phone: 707-826-3944, fax: 707-826-4060
Supplementary Table 1. Population ID, water body, sample size for microsatellites (n uSats), sample size for mitochondrial DNA (n
mtDNA), collection location, latitude/longitude, date of collection and voucher numbers for specimens deposited into the Humboldt
State University fish collection.
ID
EEL
EEL
EEL
EEL
EEL
EEL
EEL
ELK
CL
CAC
CAC
CAC
Water
Body
Eel
River
Eel
River
Eel
River
Eel
River
Eel
River
Eel
River
Eel
River
Humboldt
Bay
Clear
Lake
Cache
Cache
Cache
n
uSats
n
mtDNA
59
14
18
10
16
13
15
16
14
16
13
15
0
4
6
6
16
16
13
12
4
0
15
16
Collection Location
South Fork Eel River near
Miranda, Humboldt Co., CA
Eel River at Rio Del, Humboldt
Co., CA
Williams Creek, tributary to
Middle Fork Eel River,
Mendocino Co., CA
Black Butte River, Mendocino
Co., CA
Eel River near Dos Rios,
Humboldt Co., CA
Parimore Creek to Rice Fork of
Eel River, Humboldt County, CA
North Fork Eel River off Mina
Road, Mendocino Co., CA
Martin Slough at Eureka
Municipal Golf Course, Humboldt
Co., CA
Kelsey Creek at Kelseyville, Lake
Co., CA
Cache Creek at Rumsey, Yolo
Co., CA
Cache Creek at Guinda, Yolo Co.,
CA
North Fork Cache Creek at NFCC
State Wildlife Area, Lake Co., CA
Latitude
Longitude
Date
40o 13’ 03.91" N
123o 49’ 00.79” W
October 2004
40o 29' 53.27" N
124o 05' 26.13" W
July 2006
39 48’ 59.62" N
123 08’ 01.60" W
39o 49’ 14.61” N
123o 04’ 53.57” W
September 2011
39o 41’ 13.43” N
123° 21’ 33.52” W
September 2011
39o 19’ 36.47” N
122° 52’ 16.10” W
September 2011
39o 56’ 17.61” N
123o 20’ 55.55” W
September 2011
HSU
Accession
Number
5040
5041
September 2011
o
o
5042
August 2008,
November 2008,
July 2011
40o 45’ 27.03” N
124o 10’ 16.76” W
38o 58’ 53.91” N
122o 50’ 36.26” W
April 2009
38o 53’ 24.56” N
122o 14’ 16.66” W
October 2004,
May 2009
38o 49’ 47.43” N
122o 10’ 56.18” W
October 2004
38o 59’ 17.90” N
122o 32’ 24.26” W
March 2012
5043
5044
5045
5046
5047
5048
5049,
5050
5051
5052
Cache
1
1
CAC
CAC
CAC
CAC
SAC
SAC
SAC
PUT
PUT
PUT
RUS
Cache
2
3
Cache
3
3
Cache
0
3
Sacramento
Sacramento
Sacramento
Putah
Creek
Putah
Creek
Putah
Creek
Russian
River
16
16
47
49
0
3
0
1
0
3
0
3
56
58
North Fork Cache Creek
downstream of Indian Valley
Reservior Dam, Lake Co., CA
Indian Valley Reservoir, Lake
Co., CA
Indian Valley Reservoir, Lake
Co., CA
North Fork Cache Creek at Spring
Valley, Lake Co., CA
Sacramento River near Red Bluff,
Tehema Co., CA
Sacramento River near Red Bluff,
Tehema Co., CA
Sacramento River near Red Bluff,
Tehema Co., CA
Putah Creek near Middletown,
Lake Co., CA
Putah Creek at Coyote Valley,
Lake Co., CA
Anderson Creek near Anderson
Springs, Lake Co., CA
Russian River off Wohler Road,
Sonoma Co., CA
39o 04’ 38.92” N
122o 32’ 05.36” W
May 2009
39o 04’ 52.11” N
122o 32’ 15.72” W
September 2010
39o 10’ 01.70” N
122o 31’ 38.49” W
May 2009, March
2012
39o 04’ 25.24” N
122o 34’ 57.46” W
March 2012
40o 09’ 10.53” N
122o 12’ 00.64” W
January - March
2007
40o 09’ 10.53” N
122o 12’ 00.64” W
September 2007
40o 09’ 10.53” N
122o 12’ 00.64” W
January February 2008
38o 48’ 19.09” N
122o 36’ 52.51” W
July 2011
38o 48' 02.17” N
122o 34’ 30.85” W
April 2009
38o 46’ 38.65” N
122o 40’ 57.99” W
July 2009
38o 30’ 30.60” N
122o 52’ 59.70” W
July - August
2008
5053
5054
5055,
5056
5057
5058
5059
5060
5061
5062
5063
5064
Supplementary Table 2. Microsatellite loci details including allelic richness across all populations, size range (including amplified
flanking regions and microsatellite repeats) in base pairs (bp), cycling conditions, and references.
Locus
CYPG21
Allelic
Richness
43
Size Range
174-382
CYPG22
11
201-277
CYPG24
12
162-225
CYPG37
32
132-224
CYPG48
19
133-209
CYPG49
10
101-138
RHCA15b 16
145-190
Cycling Conditions
95 for 60 seconds, 30 cycles of: 95oC for 60 seconds,
67oC for 45 seconds with -0.5 oC/cycle, and 72oC for 120
seconds
95o for 60 seconds, 30 cycles of: 95oC for 60 seconds,
67oC for 45 seconds with -0.5 oC/cycle, and 72oC for 120
seconds
95o for 60 seconds, 30 cycles of: 95oC for 60 seconds,
67oC for 45 seconds with -0.5 oC/cycle, and 72oC for 120
seconds
95o for 60 seconds, 30 cycles of: 95oC for 60 seconds,
67oC for 45 seconds with -0.5 oC/cycle, and 72oC for 120
seconds
95o for 60 seconds, 30 cycles of: 95oC for 60 seconds,
67oC for 45 seconds with -0.5 oC/cycle, and 72oC for 120
seconds
95o for 60 seconds, 30 cycles of: 95oC for 60 seconds,
67oC for 45 seconds with -0.5 oC/cycle, and 72oC for 120
seconds
92oC for 30 seconds, 45 cycles of: 92oC for 30 seconds,
50oC for 15 seconds, 68oC for 15 seconds, and 68oC for
120 seconds
o
Reference
Baerwald, M. R., and B. May.
2004.
Baerwald, M. R., and B. May.
2004.
Baerwald, M. R., and B. May.
2004.
Baerwald, M. R., and B. May.
2004.
Baerwald, M. R., and B. May.
2004.
Baerwald, M. R., and B. May.
2004.
Girard, P., and B. Angers.
2006.
Supplementary Table 3 Source population, intrinsic rate of increase (R), number of
generations since introduction (T), carrying capacity of the introduced population (NK), estimate
of effective number of founders (NEF) in the introduced population, and lower and upper 95%
support limits.
Source
R
T
NK
NEF
95% Lower
95% Upper
CL
3
6
30000
4.3
3.3
5.7
CL
3
6
60000
4.3
3.3
5.8
CL
3
6
90000
4.4
3.3
5.7
CL
3
11
30000
4.3
3.3
5.8
CL
3
11
60000
4.3
3.3
5.8
CL
3
11
90000
4.3
3.3
5.7
CL
4
6
30000
4.3
3.3
5.7
CL
4
6
60000
4.3
3.3
5.7
CL
4
6
90000
4.3
3.3
5.7
CL
4
11
30000
4.3
3.3
5.7
CL
4
11
60000
4.3
3.3
5.8
CL
4
11
90000
4.3
3.3
5.7
CAC
3
6
30000
3.3
2.7
4.1
CAC
3
6
60000
3.3
2.7
4.1
CAC
3
6
90000
3.3
2.7
4.1
CAC
3
11
30000
3.3
2.7
4.1
CAC
3
11
60000
3.3
2.7
4.1
CAC
3
11
90000
3.3
2.7
4.1
CAC
4
6
30000
3.3
2.7
4.1
CAC
4
6
60000
3.3
2.7
4.1
CAC
4
6
90000
3.3
2.7
4.1
CAC
4
11
30000
3.3
2.7
4.1
CAC
4
11
60000
3.3
2.7
4.1
CAC
4
11
90000
3.3
2.7
4.1
SAC
3
6
30000
2.9
0
3.5
SAC
3
6
60000
2.9
0
3.5
SAC
3
6
90000
2.9
0
3.5
SAC
3
11
30000
2.9
0
3.4
SAC
3
11
60000
2.9
0
3.4
SAC
3
11
90000
2.9
0
3.4
SAC
4
6
30000
2.9
0
3.4
SAC
4
6
60000
2.9
0
3.4
SAC
4
6
90000
2.9
0
3.4
SAC
4
11
30000
2.9
0
3.4
SAC
4
11
60000
2.9
0
3.4
SAC
4
11
90000
2.9
0
3.5
Supplementary Table 4 Haplotype ID and haplotype definitions for the 17 haplotypes in our
Sacramento pikeminnow study populations.
Haplotype ID
Hap_1
Hap_2
Hap_3
Hap_4
Hap_5
Hap_6
Hap_7
Hap_8
Hap_9
Hap_10
Hap_11
Hap_12
Hap_13
Hap_14
Hap_15
Hap_16
Hap_17
Haplotype Definition
GTATAGCAAAGTATCTGTGTAA
GTACAGTAAAGTATTCGTGTAA
GTGCAATAAGGTACTCATGCGA
GTACAGTGAAGTGTTCGTGTAA
GTGCAATAAGGTACTCGTGTGA
ATGCAATAGGGTACTCGTGTGA
GTGCAATAGGGTACTCGTGTGA
GTACAGTAAAGTATTCGTGTAG
GTACAGCAAAGTATTCGTGTAA
GTGCAATAAGGTACTCGTGCGA
GTACAGTAAAATACTCGTGTAA
GTACAGTAAAGCATTCGTGTAA
GTACAGCAAAGTATCTGTGTAA
GTACGGCAAAGTATTCGTATAA
GTACAGTAAAGTATTCGCGTAA
GTACAACAAAGTATCCGTGTAA
GGACGGCAAAGTATTCGTATAA
Supplementary Table 5 Mitochondrial DNA haplotype frequencies among Sacramento
pikeminnow populations.
Haplotype: EEL
ELK
CL
CAC
SAC
PUT
RUS
Hap_1
26
0
0
7
0
0
0
Hap_2
62
6
12
25
42
3
0
Hap_3
0
0
4
5
0
2
0
Hap_4
0
0
0
1
9
0
0
Hap_5
0
0
0
0
0
0
55
Hap_6
0
0
0
0
0
0
2
Hap_7
0
0
0
0
0
0
1
Hap_8
0
0
0
0
2
0
0
Hap_9
0
0
0
0
1
0
0
Hap_10
0
0
0
0
5
0
0
Hap_11
0
0
0
0
2
0
0
Hap_12
0
0
0
0
1
0
0
Hap_13
0
0
0
0
2
0
0
Hap_14
0
0
0
0
2
1
0
Hap_15
0
0
0
0
1
0
0
Hap_16
0
0
0
0
1
0
0
Hap_17
0
0
0
0
0
1
0
Supplementary Fig. 1 Mean estimate of Ln probability of data versus assumed cluster number
(K) resulting from the Bayesian cluster methods implemented in STRUCTURE.
Supplementary Fig. 2 ΔK versus cluster number (K) resulting from Bayesian cluster analysis
implemented in STRUCTURE.